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2012: The Year When Genomic Medicine Started Paying Off

Remember a couple of years ago when people commemorated the 10-year anniversary of the first draft human genome sequencing? The storyline then, in 2010, was that we all went off to genome camp and only came home with a lousy T-shirt. Society, we were told, invested huge scientific resources in deciphering the code of life, and there wasn’t much of a payoff in the form of customized, personalized medicine.

That was an easy conclusion to reach then, when personalized medicine advocates could only point to a couple of effective targeted cancer drugs—Genentech’s Herceptin and Novartis’ Gleevec—and a couple of diagnostics. But that’s changing. My inbox the past week has been full of analyst reports from medical meetings, which mostly alerted readers to mere “incremental” advances with a number of genomic-based medicines and diagnostics. But that’s a matter of focusing on the trees, not the forest. This past year, we witnessed some really impressive progress from the early days of “clinical genomics” or “medical genomics.” The investment in deep understanding of genomics and biology is starting to look visionary.

The movement toward clinical genomics gathered steam back in June at the American Society of Clinical Oncology annual meeting. One of the hidden gem stories from ASCO was about little companies like Cambridge, MA-based Foundation Medicine and Cambridge, MA-based Knome that started seeing a surprising surge in demand from physicians for their services to help turn genomic data into medical information. The New York Times wrote a great story a month later about a young genomics researcher at Washington University in St. Louis who got cancer, had access to incredibly rich information about his tumors, and—after some wrestling with his insurance company—ended up getting a targeted drug nobody would have thought to prescribe without that information. And last month, I checked back on Stanford University researcher Mike Snyder, who made headlines this year using a smorgasbord of “omics” tools to correctly diagnose himself early with Type 2 diabetes, and then monitor his progress back into a healthy state.

Notice the pattern here—the stories here aren’t all about drugs. They are about the value of new biological information.

This month at the American Society of Hematology (ASH) meeting in Atlanta, GA, another new front opened up in the ongoing story of “clinical genomics.” A couple of small and intensely competitive private companies—Seattle-based Adaptive Biotechnologies and South San Francisco-based Sequenta—had emerged on the national stage with valuable new approaches to diagnosis and disease monitoring. It’s through what is sometimes called “immune profiling.”

A little bit of science is required here to understand what Adaptive and Sequenta are doing, and why it’s important. While the 3-billion-letter signature of DNA that makes up a human genome is consistent in almost every cell of the body, the immune system’s B cells and T cells are an exception. In these cells, DNA gets shuffled around in a vast array of new combinations, allowing T cells to recognize specific invaders such as flu viruses, and allowing B cells to generate antibodies against them.

Until recent advancements made DNA sequencing super-fast and super-cheap, nobody had any way to really look closely at the whole kaleidoscope of immune diversity, or the “immune repertoire” that resides within any individual like you or me.

But gene sequencing instruments have come a long way in the past few years, and some very smart computer programmers have crafted algorithms that can help spot the signals of disease or wellness in these big genomic data sets. This collision of technologies has made it possible for companies like Adaptive and Sequenta to take a blood sample from a patient and scan for genetic rearrangements in a low-cost, systematic way.

The possible applications here are broad. You could, in theory, use such technologies to tell whether multiple sclerosis or rheumatoid arthritis patients are likely to respond to a given therapy. You might be able to do the same thing with lung or breast cancer patients. Essentially, anybody who studies or treats diseases of the immune system—and that’s a lot of people—could find this sort of technology handy.

But at least in the beginning, both Sequenta and Adaptive are both aiming their lab-based offerings at blood cancer specialists who are on the lookout for “minimal residual disease” in their patients, and constantly wondering what to do about it. Both of these companies have partnered with high-powered scientists in the field to gather data on the usefulness of their tests. Both have gotten the standard CLIA certification they need to process blood samples at central company labs. Both are figuring out what to charge for their tests, and seeking to win reimbursement support from health insurers. Both are racing to get their diagnostic tests on the market in early 2013. And importantly, both companies came back home from ASH with a little extra mojo, as physician/researchers are looking to get on waiting lists for the services.

What’s even more surprising? At last year’s ASH, hardly anybody had heard of Adaptive or Sequenta or had the foggiest idea what they meant by “immune profiling.”

Chad Robins of Adaptive Biotechnologies

“Last year, there were a few thought leaders who were starting to explore it,” says Adaptive CEO Chad Robins. “Now, we get inquiries every day on things like, ‘When will you accept clinical samples?’ Or ‘When will this be reimbursed by insurance companies?’ Every day we get a couple. It’s all now a question of when.”

Sequenta’s CEO Tom Willis adds: “ASH for us was a coming out party for all the data we’ve been compiling.”

Doing this kind of immune-system sequencing was impossible just a few years ago, as it would have cost a few million dollars’ worth of traditional sequencing to examine immune cell diversity in just a milliliter of blood. Now we’re on the brink of having it become routine, and even affordable, as these companies are looking to compete with flow cytometry tests that cost anywhere from a few hundred bucks to $1,500 per test.

Many people surely saw one of the bigger stories this week from ASH—the New York Times report about a 6-year-old girl named Emma Whitehead who was saved by a team of researchers at the University of Pennsylvania. This heartwarming story described how Emma was near death from leukemia when scientists reprogrammed her immune system to fight off cancer cells. The girl not only lived, but the Times’ Denise Grady noted she has lately been “practicing somersaults and rugby-style tumbles that make her parents wince.” The technique didn’t lead to a happy ending for every patient in the study, but the result was still extremely encouraging.

What the story didn’t say is that researchers knew with a new degree of confidence that Emma’s cancer was really down for the count. And they knew that because of decades of investment in super-fast, super-cheap gene sequencing instruments, combined with sophisticated computer software, and a whole lot of immunology expertise at Adaptive. And you can bet that researchers will keep using the tool to look for “minimal residual disease” that might someday relapse for young Emma.

Of course, with any new technology, there are going to be caveats. Reams of studies need to be run—and they are being run—to ask whether all this information is actually leading to better treatment outcomes for patients. We need to know if these technologies are going to kick expensive imaging tests to the curb and save the health system money, or whether they are just going to add a new layer of costs. We need to know if this kind of test will enable society to get rid of excessive chemo treatments when they are truly unnecessary. We need to make sure people of all kinds can get access to these powerful new techniques.

Dysfunctional as the healthcare delivery system is, this kind of information is powerful stuff, and I believe will be a real boon to patient care for a long time. Those doctors at Penn now know that when they tell a mother and father that their 6-year-old girl is cancer-free, they aren’t just basing that on a vague result from a cell-counter, but something that can spot a one-in-a-million cancer cell. It’s an awesome thing to behold. What’s more it’s just one piece in a big, ever-expanding genomic medicine puzzle. That personalized medicine payoff may not be here yet, but it’s coming, bit by bit.

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The Author

This is indeed very interesting and highly promising reports. Is there any objective, publicly available evidence on reproducibility, reliability and concordance of these technologies akin to the type of analytics offerred reliably to patients under FDA approval?